python-microscopy 25.6.5__cp39-cp39-win_amd64.whl

PYME/experimental/fusionUtils.py

@@ -0,0 +1,522 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Jul  9 00:55:38 2015
+
+@author: david
+"""
+
+import numpy as np
+# import pylab as pl
+import matplotlib.pyplot as pl
+from PYME.IO import image
+import PYME.Analysis.Tracking.trackUtils as trackUtils
+import json
+
+def plotEvent(clump, pipeline, rawData = None, plotRaw = True):
+    pl.figure()
+    
+    vs = pipeline.mdh.voxelsize_nm.x
+    xp = int(clump['x'].mean()/vs)
+    yp = int(clump['y'].mean()/vs)
+
+    ind1 = (clump['fitError_Ag'] < 1e3)*(clump['fitError_Ag'] > 0)
+    ind2 = (clump['fitError_Ar'] < 1e3)*(clump['fitError_Ar'] > 0)*(clump['Ar'] > 100)    
+    
+    pl.subplot(311)
+    #pl.plot(clump['t'], clump['Ag']/clump['Ag'][ind1].max(), 'g')
+    pl.plot(clump['t'][ind1], clump['Ag'][ind1]/clump['Ag'][ind1].max(), 'b')
+    #ym = (2*np.pi*clump['fitResults_Ag']*(clump['fitResults_sigma']/vs)**2)
+    #pl.grid()
+    #pl.ylim(0, ym)
+    #pl.twinx()
+    #pl.plot(clump['t'], clump['Ar']/clump['Ar'][ind2].max(), 'b', alpha=.5)
+    pl.plot(clump['t'][ind2], clump['Ar'][ind2]/clump['Ar'][ind2].max(), 'g', alpha=.5)
+    #pl.plot(clump['t'], 2*np.pi*clump['fitResults_Ar']*(clump['fitResults_sigmag']/vs)**2)
+    
+
+    #ym = (2*np.pi*clump['fitResults_Ag']*(clump['fitResults_sigma']/vs)**2).max()
+    #ym2 = (2*np.pi*clump['fitResults_Ar']*(clump['fitResults_sigmag']/vs)**2).max()
+    
+    #pl.ylim(0, max(ym, ym2))
+    pl.ylim(0, 1)
+    pl.grid()
+    
+    pl.ylabel('Intensity [a.u.]')
+    pl.xlabel('Time [frames]')
+    pl.legend(['Lipid', 'Cargo'])
+    
+    pl.title('clumpIndex=%d, position = (%d, %d) px' % (clump['clumpIndex'][0], xp, yp))
+    
+    
+    pl.subplot(312)
+    pl.plot(clump['t'][ind1], clump['fitResults_sigma'][ind1])
+    pl.plot(clump['t'][ind2], clump['fitResults_sigmag'][ind2], alpha=.5)
+    
+    pl.ylim(0, 1e3)
+    pl.grid()
+    
+    pl.ylabel('Fit $\sigma$ [nm]')
+    pl.xlabel('Time [frames]')
+    pl.legend(['Lipid', 'Cargo'])
+    
+    pl.subplot(615)
+    if plotRaw:
+        rawImg = image.openImages.items()[-1][1]
+        
+        fnums = np.linspace(clump['t'].min(), clump['t'].max(), 10).astype('i')
+        frames = np.hstack([rawImg.data[(xp-10):(xp+10), (yp-10):(yp + 10), fi].squeeze() for fi in fnums])
+        pl.imshow(frames, interpolation='nearest', cmap='hot')
+        
+        pl.subplot(616)
+        xp = int((clump['x'].mean() - pipeline.mdh['chroma.dx'](0,0))/vs)
+        yp = int((clump['y'].mean() - pipeline.mdh['chroma.dy'](0,0))/vs) + 256
+        frames = np.hstack([rawImg.data[(xp-10):(xp+10), (yp-10):(yp + 10), fi].squeeze() for fi in fnums])
+        pl.imshow(frames, interpolation='nearest', cmap='hot')
+        #except:
+    #    pass
+
+
+def plotEvent2(clump, pipeline, rawData = None, plotRaw = True):
+    pl.figure()
+    
+    vs = pipeline.mdh.voxelsize_nm.x
+    xp = int(clump['x'].mean()/vs)
+    yp = int(clump['y'].mean()/vs)
+
+    ind1 = (clump['fitError_Ag'] < 1e3)*(clump['fitError_Ag'] > 0)
+    ind2 = (clump['fitError_Ar'] < 1e3)*(clump['fitError_Ar'] > 0)*(clump['Ar'] > 100)    
+    
+    pl.subplot(311)
+    #pl.plot(clump['t'], clump['Ag']/clump['Ag'][ind1].max(), 'g')
+    pl.plot(clump['t'][ind1], clump['Ag'][ind1]/clump['Ag'][ind1].max(), 'b')
+    #ym = (2*np.pi*clump['fitResults_Ag']*(clump['fitResults_sigma']/vs)**2)
+    #pl.grid()
+    #pl.ylim(0, ym)
+    #pl.twinx()
+    #pl.plot(clump['t'], clump['Ar']/clump['Ar'][ind2].max(), 'b', alpha=.5)
+    pl.plot(clump['t'][ind2], clump['Ar'][ind2]/clump['Ar'][ind2].max(), 'g', alpha=.5)
+    #pl.plot(clump['t'], 2*np.pi*clump['fitResults_Ar']*(clump['fitResults_sigmag']/vs)**2)
+    
+
+    #ym = (2*np.pi*clump['fitResults_Ag']*(clump['fitResults_sigma']/vs)**2).max()
+    #ym2 = (2*np.pi*clump['fitResults_Ar']*(clump['fitResults_sigmag']/vs)**2).max()
+    
+    #pl.ylim(0, max(ym, ym2))
+    pl.ylim(0, 1)
+    pl.grid()
+    
+    pl.ylabel('Intensity [a.u.]')
+    pl.xlabel('Time [frames]')
+    pl.legend(['Lipid', 'Cargo'])
+    
+    pl.title('clumpIndex=%d, position = (%d, %d) px' % (clump['clumpIndex'][0], xp, yp))
+    
+    
+    pl.subplot(312)
+    pl.plot(clump['t'][ind1], clump['fitResults_sigma'][ind1])
+    pl.plot(clump['t'][ind2], clump['fitResults_sigmag'][ind2], alpha=.5)
+    
+    pl.ylim(0, 1e3)
+    pl.grid()
+    
+    pl.ylabel('Fit $\sigma$ [nm]')
+    pl.xlabel('Time [frames]')
+    pl.legend(['Lipid', 'Cargo'])
+    
+    pl.subplot(615)
+    if plotRaw:
+        rawImg = image.openImages.items()[-1][1]
+        
+        fnums = np.linspace(clump['t'].min(), clump['t'].max(), 10).astype('i')
+        frames = np.hstack([rawImg.data[(xp-10):(xp+10), (yp-10):(yp + 10), fi].squeeze() for fi in fnums])
+        pl.imshow(frames, interpolation='nearest', cmap='hot')
+        
+        pl.subplot(616)
+        xp = int((clump['x'].mean() - pipeline.mdh['chroma.dx'](0,0))/vs)
+        yp = int((clump['y'].mean() - pipeline.mdh['chroma.dy'](0,0))/vs) + 256
+        frames = np.hstack([rawImg.data[(xp-10):(xp+10), (yp-10):(yp + 10), fi].squeeze() for fi in fnums])
+        pl.imshow(frames, interpolation='nearest', cmap='hot')
+        #except:
+    #    pass
+
+def plotEvent3(clump, rawData = None, fitRes = None):
+    from scipy import ndimage
+    
+    dt = 18.27
+    pl.figure()
+    pl.subplot(211)
+    
+    c = clump
+    if not fitRes is None:
+        t0 = fitRes['t0']
+    else:
+        t0 = 0
+        
+    i1 = abs(c['fitError_Ag']) < 500
+    
+    t = c['t'][i1]
+    I = c['Ag'][i1]
+
+    t = np.hstack([t[0] - 1, t])
+    I = np.hstack([0, I])    
+    
+    pl.plot((t - t0)*dt, ndimage.median_filter(I, 3), lw=4)
+    
+    
+    pl.plot([0,0], pl.ylim(), 'k:')
+    
+    pl.yticks([])
+    
+    pl.xlim(-20*dt, 100*dt)
+    
+    pl.xticks([])
+    #pl.axes()
+    pl.box()
+
+    
+    pl.subplot(212)
+    
+    i2 = (abs(c['fitError_Ar']/c['fitResults_Ar']) < 2)*(c['fitResults_sigmag'] > 100)
+    pl.plot((c['t'][i2] - t0)*dt, ndimage.median_filter(c['Ar'][i2], 3), 'r', lw=4)
+    pl.xlim(-20*dt, 100*dt)
+    pl.yticks([])
+    pl.plot([0,0], pl.ylim(), 'k:')
+    
+    ysb = .2*np.mean(pl.ylim())
+    pl.plot([1500, 1700], [ysb, ysb], 'k', lw=8)
+    pl.text(1500, ysb + .6*ysb, '200 ms')
+    pl.xticks([])
+    #pl.axes()
+    pl.box()
+    
+    pl.figure()
+    
+    tvals = np.array([-20, -5, 1, 5, 10, 20, 50, 100]) + int(t0)
+    vs = clump.pipeline.mdh.voxelsize_nm.x
+    xp = int(clump['x'].mean()/vs)
+    yp = int(clump['y'].mean()/vs)
+    
+    xp1 = int((clump['x'].mean() - clump.pipeline.mdh['chroma.dx'](0,0))/vs)
+    yp1 = int((clump['y'].mean() - clump.pipeline.mdh['chroma.dy'](0,0))/vs) + 256
+    
+
+    lMax = 1.0*rawData[max(xp-10, 0):(xp+10), max(yp-10, 0):(yp + 10), tvals[3]].max()
+    lMin = 1.0*rawData[max(xp-10, 0):(xp+10), max(yp-10, 0):(yp + 10), tvals[0]].min()
+
+    cMax = 1.0*rawData[max(xp1-10, 0):(xp1+10), max(yp1-10, 0):(yp1 + 10), tvals[4]].max()
+    cMin = 1.0*rawData[max(xp1-10, 0):(xp1+10), max(yp1-10, 0):(yp1 + 10), tvals[0]].min()     
+         
+    
+    for i, t_i in enumerate(tvals):
+        pl.subplot(2,8,i+1)
+        frame = rawData[max(xp-10, 0):(xp+10), max(yp-10, 0):(yp + 10), t_i].squeeze()        
+        #pl.imshow(frame, interpolation='nearest', cmap='hot', clim=(lMin, lMax))
+        
+        fr = 1.0 - np.clip(((frame - lMin)/float(lMax - lMin)), 0, 1)[:,:,None]*np.array([1, 1, .5])[None, None, :]
+        pl.imshow(fr, interpolation='nearest')
+        pl.xticks([])
+        pl.yticks([])
+        
+        pl.subplot(2,8,i+8 + 1)
+        frame = rawData[max(xp1-10, 0):(xp1+10), max(yp1-10, 0):(yp1 + 10), t_i].squeeze()        
+        #pl.imshow(frame, interpolation='nearest', cmap='hot', clim=(cMin, cMax))
+        fr = 1.0 - np.clip(((frame - cMin)/float(cMax - cMin)), 0, 1)[:,:,None]*np.array([.5, 1, 1])[None, None, :]
+        pl.imshow(fr, interpolation='nearest')
+        pl.xticks([])
+        pl.yticks([])
+        
+    pl.tight_layout(pad=.5)
+        
+
+from PYME.Analysis._fithelpers import FitModel, FitModelWeighted
+
+def widthMod(p, t, w0=225.):
+    """model for width of lipid signal used to detect the time of fusion as
+    indicated by the onset of the lipid difusion into the membrane
+    
+    the model takes two variable parameters: 
+        t0: the time of fusion
+        adiff: a scaling factor proportional to the diffusion constant in the membrane
+        
+    In addition, there is one fixed parameter:
+        w0: the width of a vesicle before fusion. For diffraction limited vesicles,
+            this should be constant over all vesicles. In this case, the value was
+            determined by visual inspecton of a number of traces.
+    """
+    t0, adiff = p
+    
+    return w0 + np.sqrt(np.maximum(adiff*(t-t0), 0))
+
+def lipidMod(p, t, t0):
+    """This is the lipid signal model from the paper (Eqn ?). The main difference
+    is that I have extended the fitting to just before fusion (in the cases where
+    fusion and docking do not occur simultaeneously) to allow better estimation
+    of Ifus.
+
+    The model is hence: Ifus if t < t0
+                        Ifus*(all the rest) if t >= t0
+                        
+    The variable parameters are:
+        tb: the bleaching lifetime
+        trel: release time
+        lTIRF: the intensiy factor
+        Ifus: the intensity imediately prior to fusion
+        
+    An aditional fixed parameter:
+        t0: the time of fusion (determined by fitting the knee in the vesicle width curve)
+    
+    """
+    tb, trel, lTIRF, Ifus = p
+    
+    t = t - t0    
+    
+    return Ifus*((t<0) + (t>=0)*(np.exp(-t/trel) + (np.exp(-t/tb) - np.exp(-t/trel))/(lTIRF*(1-trel/tb))))
+    
+def cargoMod(p, t, t0, Ib = 0):
+    """This is an emperical model for the content release events.
+    
+    It consists of:
+        - A  $1-e^(-t/trel)$ dequenching term
+        - A standard $e^-(t/tbl)$ bleaching term
+        - And a burst or detachment term. The 'burst' happens at the timepoint tbr
+          and follows the same kinetics as the initial dequenching. When fitting, 
+          tbr is initialised to be very long, so it should only ever take effect
+          when there is actually a 'turn off' signal.
+          
+    This takes 2 fixed parameters:
+        t0: time of fusion
+        Ib: background intensity
+          
+    """
+        
+    I0, trel, tbl, tbr = p
+    
+    return Ib + I0*(1-np.exp(-(t-t0)/trel))*(t>t0)*np.exp(-(t-t0)/tbl)*(1-np.exp(-(tbr - t)/trel))*(t < tbr) 
+    
+def fitIntensities(clump):
+    from scipy import ndimage 
+    pl.figure(figsize=(9, 9))
+    
+    pl.subplot(311)
+    
+    ind1 = (clump['fitError_Ag'] < 1e3)*(clump['fitError_Ag'] > 0)
+    ind2 = (clump['fitError_Ar'] < 1e3)*(clump['fitError_Ar'] > 0)*(clump['Ar'] > 100) 
+    
+    try:    
+        t0_guess = np.where(ndimage.median_filter(clump['sig'], 5) > 400)[0][0]
+    except IndexError:
+        t0_guess = 10
+        
+    #print t0_guess
+
+    #fit to clump widths to find initial 'knee' - ie fusion time    
+    t = clump['t'][ind1][max(t0_guess - 20, 0):(t0_guess + 40)].astype('f')
+    w = clump['fitResults_sigma'][ind1][max(t0_guess - 20, 0):(t0_guess + 40)]
+    s = clump['fitError_sigma'][ind1][max(t0_guess - 20, 0):(t0_guess + 40)]
+    
+    pl.plot(clump['t'][ind1], clump['fitResults_sigma'][ind1])
+    
+    rw = FitModelWeighted(widthMod, [t.min() + 20., 100.], w, s, t)
+    #print rw[0]
+    
+    t0, adiff = rw[0]
+    
+    t0 = max(t0, t.min())
+    pl.plot(t, widthMod(rw[0], t), lw=3)
+    pl.ylabel('Lipid width ($\sigma$) [nm]')
+    pl.xlabel('Time [frames]')
+    pl.grid()
+    
+    pl.title('clumpIndex=%d' % (clump['clumpIndex'][0], ))    
+    
+    ###################    
+    # Lipid Intensity
+    
+    pl.subplot(312)
+    #pl.plot(clump['t'], clump['Ag']/clump['Ag'][ind1].max(), 'g')
+
+    t = clump['t'][ind1].astype('f')
+    #t = t - t.min()
+    I = clump['Ag'][ind1]
+    s = clump['fitError_Ag']*(clump['fitResults_sigma']**2)*clump.pipeline.mapping.a_norm
+    s = s[ind1] 
+    
+    Inorm = I[((t-t0) < 10)*(t> (t0+2))].mean()
+    
+    
+    #plot raw data
+    pl.plot(t, I/Inorm, 'x-')
+    
+    #select a region and fit to the lipid model
+    i3 = ((t-t0) > -10)*((t-t0) < 100)
+    
+    pfit = FitModelWeighted(lipidMod, [300., 3, .2, I[(t-t0) <=0].mean()], I[i3], s[i3], t[i3], t0)
+    #print pfit[0]
+    
+    #plot fit results
+    t_ = np.arange(t[i3].min(), t[i3].max()).astype('f')
+    pl.plot(t_, lipidMod(pfit[0], t_, t0)/Inorm, lw=3)
+    pl.text((t.mean() + t[-1])/2, .5, '$t_0=%3.1f$\n$\\tau_{bleach}=%3.1f$\n$\\tau_{rel}=%3.2f$\n$\lambda_{TIRF}=%3.2f$' % tuple([t0,] + list(pfit[0][:3])), bbox=dict(facecolor='white', alpha=0.8, edgecolor='white'))
+    #pl.text((t.mean() + t[-1])/2, .5, '$I_0=%3.1f$\n$\\tau_{rel}=%3.1f$\n$\\tau_{bl}=%3.2f$\n$t_{burst}=%3.2f$' % tuple(list(pfitC[0])), bbox=dict(facecolor='white', alpha=0.8, edgecolor='white'))
+    #pl.plot(t, lipidMod([300., 3, .2, .2*I.max()], t, t.min())/I.max(), 'b')
+
+    pl.ylim(0, 1.3)
+    pl.grid()
+    
+    pl.ylabel('Lipid Intensity [a.u.]')
+    pl.xlabel('Time [frames]')    
+    
+    pl.subplot(313)
+    
+    ###############
+    #Cargo
+    
+    t = clump['t'][ind2].astype('f')
+    #t = t - t.min()
+    I = clump['Ar'][ind2]
+    s = clump['fitError_Ar']*(clump['fitResults_sigmag']**2)*clump.pipeline.mapping.a_norm
+    s = s[ind2]
+    
+    Inorm = I[((t-t0) < 20)*(t> (t0+5))].mean()
+    #Ib = np.median(I[t<t0])
+    Ib = min(I)
+    
+    pl.plot(t, clump['Ar'][ind2]/Inorm, '+-', alpha=.5)
+    
+    
+    #select a region to fit over
+    i3 = ((t-t0) > -10)*((t-t0) < 150)
+    
+    #do the fit
+    pfitC = FitModelWeighted(cargoMod, [Inorm, 5., 500., 500.+ t0], I[i3], s[i3], t[i3], t0, Ib)
+    
+    #print pfitC[0]
+    
+    #plot the fit results
+    t_ = np.arange(t[i3].min(), t[i3].max()).astype('f')
+    pl.plot(t_, cargoMod(pfitC[0], t_, t0, Ib)/Inorm, lw=2)
+    
+    
+    pl.text((t.mean() + t[-1])/2, .5, '$I_0=%3.1f$\n$\\tau_{rel}=%3.1f$\n$\\tau_{bl}=%3.2f$\n$t_{burst}=%3.2f$' % tuple(list(pfitC[0])), bbox=dict(facecolor='white', alpha=0.8, edgecolor='white'))    
+    #pl.plot(t_, cargoMod([Inorm, 5., 500., 50.+ t0], t_, t0, Ib)/Inorm, lw=2)
+    
+    pl.ylim(0, 1.3)
+    pl.grid()
+    
+    pl.ylabel('Cargo Intensity [a.u.]')
+    pl.xlabel('Time [frames]')
+    #pl.legend(['Lipid', 'fit', 'Cargo', 'fit'])
+    
+    ############
+    # Package up our fit results
+    d = {}
+    d['t0'], d['bdiffuse'] = rw[0]
+    d['tb_lip'], d['trel_lip'], d['lTIRF_lip'], d['Ifus_lip'] = pfit[0]
+    d['I0_cargo'], d['trel_cargo'], d['tbl_cargo'], d['tbr_cargo'] = pfitC[0]
+    
+    return d
+    
+   
+def prepPipeline(pipeline):
+    #we fit peak intensity - define mappings which are propotional to integrated intensity instead
+    pipeline.mapping.a_norm = 2*np.pi/(pipeline.mdh.voxelsize_nm.x)**2
+    pipeline.mapping.setMapping('Ag', 'a_norm*fitResults_Ag*fitResults_sigma**2')
+    pipeline.mapping.setMapping('Ar', 'a_norm*fitResults_Ar*fitResults_sigmag**2')
+    
+    #choose 'plausible' fits    
+    pipeline.filterKeys = {'A': (5, 20000), 'sig': (95.0, 1500)}
+    pipeline.Rebuild()
+    
+    #perform tracking
+    #this is simple event chaining which works well for well separated events
+    #here we connect everything which is within 500 nm, allowing temporal gaps of up to 5 frames 
+    trackUtils.findTracks(pipeline, '1.0',500, 5)
+    
+    #tracking introduces two new variables into the pipeline - clumpIndex (which
+    #is a unique identifier for the particular track), and clumpSize (which is the length of the track)    
+    
+    #select only the tracks which have more than 100 frames
+    pipeline.filterKeys['clumpSize'] =  (100.0, 100000.0)
+    pipeline.Rebuild()
+    
+
+def selectAndPlotEvents(pipeline, outputdir='/Users/david/FusionAnalysis', speckleFile = None):
+    import os
+    import pandas as pd
+    from PYME.IO.FileUtils.readSpeckle import readSpeckles    
+    #now iterate through our clumps
+    clumpIndices = list(set(pipeline['clumpIndex']))
+    
+    clumps = [pipeline.clumps[i] for i in clumpIndices]
+    
+    
+    
+    if not speckleFile is None: #use speckle file to determine which tracks correspond to fusion events
+        vs = pipeline.mdh.voxelsize_nm.x
+        speckles = readSpeckles(speckleFile)
+        
+        #print speckles
+        
+        sp = np.array([s[0,:] for s in speckles])
+        #print sp.shape
+        
+        #filteredClumps = [c for c in clumps if (((c['x'][0] - vs*sp[:,1])**2 + (c['y'][0] - vs*sp[:,0])**2 + (5*(c['t'][0] - sp[:,2]))**2).min() < 300**2)]
+        
+        #find those clumps which are near (< 1um) to events identified in Joergs speckle file        
+        filteredClumps = [c for c in clumps if (((c['x'][0] - vs*sp[:,1])**2 + (c['y'][0] - vs*sp[:,0])**2).min() < 1000**2)]
+    
+    else:
+        #do another level of filtering - fusion events expand, so we're looking for larger than normal
+        #sigma in the lipid channel. We can also add a constraint on the mean intensity as proper docking
+        #and fusion events are brighter than a lot of the point-like rubbish
+        #We do this here, so we can filter on the aggregate behaviour of a track and be more resiliant against
+        #noise.
+        
+        filteredClumps = [c for c in clumps if (c['Ag'].mean() > 2000) and (c['fitResults_sigma'].mean() > 300)]
+            
+    outputDir = os.path.join(outputdir, os.path.split(pipeline.filename)[1])
+    if not os.path.exists(outputDir):
+        os.makedirs(outputDir)
+    
+    for c in filteredClumps:
+        plotEvent(c, pipeline, plotRaw=True)
+        pl.savefig('%s/track%d.pdf' % (outputDir, c['clumpIndex'][0]))
+        
+        r = fitIntensities(c)
+        pl.savefig('%s/track%d_fits.pdf' % (outputDir, c['clumpIndex'][0]))
+        
+        r['filename'] = os.path.split(pipeline.filename)[1]
+        r['clumpIndex'] = c['clumpIndex'][0]
+        
+        d = {}
+        d.update(c)
+        pd.DataFrame(d).to_csv('%s/track%d.csv' % (outputDir, c['clumpIndex'][0]))
+        #pd.DataFrame(r).to_csv('%s/track%d_fitResults.csv' % (outputDir, c['clumpIndex'][0]))
+        with open('%s/track%d_fitResults.json' % (outputDir, c['clumpIndex'][0]), 'w') as f:        
+            json.dump(r, f)
+        
+    return filteredClumps
+    
+    
+def main():
+    import sys
+    from PYME.LMVis import pipeline
+    from PYME.IO.image import ImageStack     
+    
+    resultFile, imageFile, speckles = sys.argv[1:]
+    
+    pipe = pipeline.Pipeline()
+    pipe.OpenFile(resultFile)
+    
+    prepPipeline(pipe)
+    
+    img = image.ImageStack(filename=imageFile, mdh='/Users/david/Downloads/JN150629c3_4_MMStack_Pos0.ome.md')
+    selectAndPlotEvents(pipe, speckleFile = speckles)
+    
+    
+if __name__ == '__main__':
+    main()
+    
+    
+    
+    

PYME/experimental/isosurface.py

@@ -0,0 +1,147 @@
+import numpy as np
+
+from . import modified_marching_cubes
+from . import marching_cubes
+
+def isosurface(data, isolevel, voxel_size=None, origin=None, remesh=False):
+    """
+    Wrapper function around modified marching cubes to generate an isosurface mesh from an image volume
+    """
+    from PYME.experimental import _triangle_mesh as triangle_mesh
+    if not voxel_size:
+        voxel_size=1.0
+
+    if not origin:
+        origin = (0,0,0)
+        
+    # FIXME - this has a silly memory overhead - write a better version of marching cubes
+    #vertices, values = marching_cubes.image_to_vertex_values(data, voxelsize=voxel_size)
+    
+    #MC = modified_marching_cubes.ModifiedMarchingCubes(isolevel)
+    #MC = marching_cubes.MarchingCubes(isolevel)
+    #MC.set_vertices(vertices, values)
+    #T = triangle_mesh.TriangleMesh.from_np_stl(MC.march())
+    
+    #MC = marching_cubes.RasterMarchingCubes(data, isolevel, voxelsize=voxel_size)
+    MC = modified_marching_cubes.RasterMarchingCubes(data, isolevel, voxelsize=voxel_size)
+    T = triangle_mesh.TriangleMesh.from_np_stl(MC.march(), origin=origin)
+    
+    if remesh:
+        # remesh to get a more uniform triangle size
+        # target edge length = 1/2 voxel size
+        if np.isscalar(voxel_size):
+            target_edge_length = voxel_size
+        else:
+            target_edge_length = np.min(voxel_size)      
+        T.remesh(target_edge_length=target_edge_length)
+    
+    return T
+
+# def triangle_sdf(p, pv):
+#     """point plane distance
+
+#     Parameters
+#     ----------
+#     p : np.array
+#         Nx(x,y,z) points
+#     pv : np.array
+#         NxMx(v0,v1,v2)x(x,y,z) triangle vertex x coordinates
+#     """
+#     # M = number of faces to average over (see distance_to_mesh)
+#     p1p0 = pv[:,:,1] - pv[:,:,0]    # (N x M x (x,y,z))
+#     p2p0 = pv[:,:,2] - pv[:,:,0]    # (N x M x (x,y,z))
+#     n = np.cross(p1p0,p2p0,axis=2)  # (N x M x (x,y,z))
+#     nn = np.linalg.norm(n,axis=2)   # (N x M)
+#     nh = n/nn[...,None]             # (N x M x (x,y,z))
+#     nh[nn==0] = 0 
+#     return (-nh*(p[:,None,:]-pv[:,:,0])).sum(2)  # (N x M)
+
+def triangle_sdf(p, pv):
+    """https://iquilezles.org/www/articles/distfunctions/distfunctions.htm
+
+    Parameters
+    ----------
+    p : np.array
+        Nx(x,y,z) points
+    pv : np.array
+        NxMx(v0,v1,v2)x(x,y,z) triangle vertex x coordinates
+    """
+    ba = pv[:,:,1] - pv[:,:,0]  
+    cb = pv[:,:,2] - pv[:,:,1]
+    ac = pv[:,:,0] - pv[:,:,2]
+    pa = p[:,None,:] - pv[:,:,0]
+    pb = p[:,None,:] - pv[:,:,1]
+    pc = p[:,None,:] - pv[:,:,2]
+    nor = np.cross(ba,ac,axis=2) 
+
+    s0 = np.sign((np.cross(ba,nor,axis=2)*pa).sum(2))
+    s1 = np.sign((np.cross(cb,nor,axis=2)*pb).sum(2))
+    s2 = np.sign((np.cross(ac,nor,axis=2)*pc).sum(2))
+    cond = (s0+s1+s2)>=2.0
+
+    c0 = ba*np.clip((ba*pa).sum(2)/(ba*ba).sum(2),0.0,1.0)[:,:,None]-pa
+    c1 = cb*np.clip((cb*pb).sum(2)/(cb*cb).sum(2),0.0,1.0)[:,:,None]-pb
+    c2 = ac*np.clip((ac*pc).sum(2)/(ac*ac).sum(2),0.0,1.0)[:,:,None]-pc
+
+    m = np.minimum(np.minimum((c0*c0).sum(2),(c1*c1).sum(2)),(c2*c2).sum(2))
+    norpa = (-nor*pa).sum(2)  # flip the sign so inside the mesh looks like outside
+                              # trick 2 from https://iquilezles.org/www/articles/interiordistance/interiordistance.htm
+    g = norpa*norpa/(nor*nor).sum(2)
+
+    m[cond] = g[cond]
+
+    s = np.sign(norpa)
+
+    return s*np.sqrt(m)
+
+def sdf_min(sdf, smooth=True, k=0.1):
+    # TODO: Default value of k=0.1 is very much arbitrary. Is there a better choice?
+    # Means the function is smoothed by ~1/10 nm
+    if smooth:
+        # Exponentially smoothed minimum
+        # https://iquilezles.org/www/articles/smin/smin.htm
+        val = -np.log2(np.nansum(np.exp2(-k*sdf), axis=1))/k
+        val[np.isnan(val)] = 0  # log2 of 0 or a negative number, shouldn't happen
+        return val
+    else:
+        return np.min(sdf, axis=1)
+
+def distance_to_mesh(points, surf, smooth=False, smooth_k=0.1, tree=None):
+    """
+    Calculate the distance to a mesh from points in a tabular dataset 
+
+    Parameters
+    ----------
+        points : np.array
+            3D point cloud to fit (nm).
+        surf : PYME.experimental._triangle_mesh
+            Isosurface
+        smooth : bool
+            Smooth distance to mesh?
+        smooth_k : float
+            Smoothing constant, by default 0.1 = smoothed by 1/10 nm
+        tree : scipy.spatial.cKDTree
+            Optionally pass a tree of face centers to use if calling
+            this function multiple times.
+    """
+
+    if tree is None:
+        import scipy.spatial
+
+        # Create a list of face centroids for search
+        face_centers = surf._vertices['position'][surf.faces].mean(1)
+
+        # Construct a kdtree over the face centers
+        tree = scipy.spatial.cKDTree(face_centers)
+
+    # Get M closet face centroids for each point
+    M = 5
+    _, _faces = tree.query(points, k=M, workers=-1)
+    
+    # Get position representation
+    _v = surf.faces[_faces]
+    v = surf._vertices['position'][_v]  # (n_points, M, (v0,v1,v2), (x,y,z))
+
+    # the negative reverses the norpa sign flip
+    # trick 2 from https://iquilezles.org/www/articles/interiordistance/interiordistance.htm
+    return -sdf_min(triangle_sdf(points, v), smooth=smooth, k=smooth_k)